rs4905475

Variant names:

• chr14-96255513-G-C
• rs4905475
• ENST00000553811.1:c.75-7139G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-96255513-G-C
• chr14-96255513-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553811.1(ENSG00000258691):​c.75-7139G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,238 control chromosomes in the GnomAD database, including 496 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.067 (496 hom., cov: 32)
• Consequence: ENSG00000258691 ENST00000553811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

Genes affected

ENSG00000258691 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258691	ENST00000553811.1	c.75-7139G>C		intron_variant	Intron 2 of 3	2		ENSP00000450984.1
ENSG00000258691	ENST00000555847.1	n.256-7139G>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10132 AN: 152122 Hom.: 495 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0666 AC: 10132 AN: 152238 Hom.: 496 Cov.: 32 AF XY: 0.0668 AC XY: 4973 AN XY: 74424

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0640

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0472 Hom.: 43

Bravo AF: 0.0576

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.21
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4905475; hg19: chr14-96721850;